Trait: visual acuity measurement

Experimental Factor Ontology (EFO) Information
Identifier EFO_0008385
Description quantification of visual acuity
Trait category
Other measurement
Mapped term PMID:28835685

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001890
(portability-PLR_avMSE)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 avMSE visual acuity measurement 44,864
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001890/ScoringFiles/PGS001890.txt.gz
PGS001985
(portability-PLR_logMAR)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 logMAR in round (left/right) visual acuity measurement 223
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001985/ScoringFiles/PGS001985.txt.gz
PGS002103
(portability-ldpred2_avMSE)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 avMSE visual acuity measurement 833,170
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002103/ScoringFiles/PGS002103.txt.gz
PGS003493
(cont-decay-avMSE)
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 avMSE visual acuity measurement 979,739
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS003493/ScoringFiles/PGS003493.txt.gz
PGS004431
(X4290.score)
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Duration screen displayed visual acuity measurement 1,059,939
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS004431/ScoringFiles/PGS004431.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM010004 PGS001890
(portability-PLR_avMSE)
 PSS009386|
European Ancestry|
4,208 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.3416 [0.3146, 0.3681] sex, age, birth date, deprivation index, 16 PCs —
PPM010005 PGS001890
(portability-PLR_avMSE)
 PSS009160|
European Ancestry|
1,144 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.3333 [0.2803, 0.3843] sex, age, birth date, deprivation index, 16 PCs —
PPM010006 PGS001890
(portability-PLR_avMSE)
 PSS008714|
European Ancestry|
2,005 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.3002 [0.2596, 0.3397] sex, age, birth date, deprivation index, 16 PCs —
PPM010007 PGS001890
(portability-PLR_avMSE)
 PSS008488|
Greater Middle Eastern Ancestry|
440 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2562 [0.1645, 0.3434] sex, age, birth date, deprivation index, 16 PCs —
PPM010008 PGS001890
(portability-PLR_avMSE)
 PSS008266|
South Asian Ancestry|
2,632 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2318 [0.1952, 0.2677] sex, age, birth date, deprivation index, 16 PCs —
PPM010009 PGS001890
(portability-PLR_avMSE)
 PSS008044|
East Asian Ancestry|
634 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.1646 [0.0866, 0.2406] sex, age, birth date, deprivation index, 16 PCs —
PPM010010 PGS001890
(portability-PLR_avMSE)
 PSS007830|
African Ancestry|
1,331 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.1066 [0.0527, 0.1598] sex, age, birth date, deprivation index, 16 PCs —
PPM010011 PGS001890
(portability-PLR_avMSE)
 PSS008934|
African Ancestry|
1,910 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.0914 [0.0465, 0.1359] sex, age, birth date, deprivation index, 16 PCs —
PPM010755 PGS001985
(portability-PLR_logMAR)
 PSS009425|
European Ancestry|
4,973 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): 0.0683 [0.0405, 0.0959] sex, age, birth date, deprivation index, 16 PCs —
PPM010757 PGS001985
(portability-PLR_logMAR)
 PSS008753|
European Ancestry|
2,200 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): 0.0178 [-0.0242, 0.0598] sex, age, birth date, deprivation index, 16 PCs —
PPM010758 PGS001985
(portability-PLR_logMAR)
 PSS008527|
Greater Middle Eastern Ancestry|
473 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): 0.0533 [-0.039, 0.1447] sex, age, birth date, deprivation index, 16 PCs —
PPM010759 PGS001985
(portability-PLR_logMAR)
 PSS008305|
South Asian Ancestry|
2,803 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): -0.0076 [-0.0447, 0.0296] sex, age, birth date, deprivation index, 16 PCs —
PPM010760 PGS001985
(portability-PLR_logMAR)
 PSS008082|
East Asian Ancestry|
698 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): -0.0376 [-0.1126, 0.0378] sex, age, birth date, deprivation index, 16 PCs —
PPM010761 PGS001985
(portability-PLR_logMAR)
 PSS007869|
African Ancestry|
1,407 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): 0.0259 [-0.0268, 0.0784] sex, age, birth date, deprivation index, 16 PCs —
PPM010762 PGS001985
(portability-PLR_logMAR)
 PSS008973|
African Ancestry|
2,025 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): -0.0189 [-0.0627, 0.0249] sex, age, birth date, deprivation index, 16 PCs —
PPM010756 PGS001985
(portability-PLR_logMAR)
 PSS009199|
European Ancestry|
1,340 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: logMAR in round (left/right) — — Partial Correlation (partial-r): 0.0299 [-0.0241, 0.0837] sex, age, birth date, deprivation index, 16 PCs —
PPM011680 PGS002103
(portability-ldpred2_avMSE)
 PSS009386|
European Ancestry|
4,208 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.3473 [0.3203, 0.3736] sex, age, birth date, deprivation index, 16 PCs —
PPM011681 PGS002103
(portability-ldpred2_avMSE)
 PSS009160|
European Ancestry|
1,144 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.3219 [0.2685, 0.3734] sex, age, birth date, deprivation index, 16 PCs —
PPM011682 PGS002103
(portability-ldpred2_avMSE)
 PSS008714|
European Ancestry|
2,005 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2905 [0.2497, 0.3303] sex, age, birth date, deprivation index, 16 PCs —
PPM011683 PGS002103
(portability-ldpred2_avMSE)
 PSS008488|
Greater Middle Eastern Ancestry|
440 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2346 [0.1421, 0.3231] sex, age, birth date, deprivation index, 16 PCs —
PPM011684 PGS002103
(portability-ldpred2_avMSE)
 PSS008266|
South Asian Ancestry|
2,632 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.2366 [0.2001, 0.2725] sex, age, birth date, deprivation index, 16 PCs —
PPM011685 PGS002103
(portability-ldpred2_avMSE)
 PSS008044|
East Asian Ancestry|
634 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.1513 [0.073, 0.2277] sex, age, birth date, deprivation index, 16 PCs —
PPM011687 PGS002103
(portability-ldpred2_avMSE)
 PSS008934|
African Ancestry|
1,910 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.0959 [0.051, 0.1404] sex, age, birth date, deprivation index, 16 PCs —
PPM011686 PGS002103
(portability-ldpred2_avMSE)
 PSS007830|
African Ancestry|
1,331 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: avMSE — — Partial Correlation (partial-r): 0.0923 [0.0384, 0.1457] sex, age, birth date, deprivation index, 16 PCs —
PPM017421 PGS003493
(cont-decay-avMSE)
 PSS010892|
European Ancestry|
4,334 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.12 sex, age, deprivation index, PC1-16 —
PPM017505 PGS003493
(cont-decay-avMSE)
 PSS010808|
European Ancestry|
1,138 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.1 sex, age, deprivation index, PC1-16 —
PPM017589 PGS003493
(cont-decay-avMSE)
 PSS010640|
European Ancestry|
1,952 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.08 sex, age, deprivation index, PC1-16 —
PPM017673 PGS003493
(cont-decay-avMSE)
 PSS010556|
Greater Middle Eastern Ancestry|
432 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.05 sex, age, deprivation index, PC1-16 —
PPM017757 PGS003493
(cont-decay-avMSE)
 PSS010220|
European Ancestry|
467 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.11 sex, age, deprivation index, PC1-16 —
PPM017841 PGS003493
(cont-decay-avMSE)
 PSS010472|
South Asian Ancestry|
2,604 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.06 sex, age, deprivation index, PC1-16 —
PPM017925 PGS003493
(cont-decay-avMSE)
 PSS010388|
East Asian Ancestry|
631 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.03 sex, age, deprivation index, PC1-16 —
PPM018009 PGS003493
(cont-decay-avMSE)
 PSS010304|
African Ancestry|
1,322 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM018093 PGS003493
(cont-decay-avMSE)
 PSS010724|
African Ancestry|
1,891 individuals
 PGP000457 |
Ding Y et al. bioRxiv (2022)
|Pre		 Reported Trait: avMSE — — partial-R2: 0.01 sex, age, deprivation index, PC1-16 —
PPM020546 PGS004431
(X4290.score)
 PSS011364|
European Ancestry|
56,192 individuals
 PGP000561 |
Jung H et al. Commun Biol (2024)
 Reported Trait: Duration screen displayed — — PGS R2 (no covariates): 0.11498 — —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS009160 — — 1,144 individuals — European Poland (NE Europe) UKB —
PSS008266 — — 2,632 individuals — South Asian India (South Asia) UKB —
PSS008527 — — 473 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009425 — — 4,973 individuals — European UK (+ Ireland) UKB —
PSS010808 — — 1,138 individuals,
36.0 % Male samples
 Mean = 54.7 years
Sd = 8.0 years		 European Polish UKB —
PSS010556 — — 432 individuals,
56.0 % Male samples
 Mean = 52.8 years
Sd = 8.2 years		 Greater Middle Eastern (Middle Eastern, North African or Persian) Iranian UKB —
PSS008934 — — 1,910 individuals — African unspecified Nigeria (West Africa) UKB —
PSS010304 — — 1,322 individuals,
37.0 % Male samples
 Mean = 52.8 years
Sd = 7.9 years		 African American or Afro-Caribbean Caribbean UKB —
PSS008044 — — 634 individuals — East Asian China (East Asia) UKB —
PSS009199 — — 1,340 individuals — European Poland (NE Europe) UKB —
PSS008305 — — 2,803 individuals — South Asian India (South Asia) UKB —
PSS008714 — — 2,005 individuals — European Italy (South Europe) UKB —
PSS010724 — — 1,891 individuals,
43.0 % Male samples
 Mean = 52.2 years
Sd = 8.1 years		 African unspecified Nigerian UKB —
PSS008973 — — 2,025 individuals — African unspecified Nigeria (West Africa) UKB —
PSS010472 — — 2,604 individuals,
54.0 % Male samples
 Mean = 53.6 years
Sd = 8.4 years		 South Asian Indian UKB —
PSS008082 — — 698 individuals — East Asian China (East Asia) UKB —
PSS010220 — — 467 individuals,
43.0 % Male samples
 Mean = 58.9 years
Sd = 6.9 years		 European Ashkenazi UKB —
PSS007830 — — 1,331 individuals — African American or Afro-Caribbean Carribean UKB —
PSS011364 — — 56,192 individuals — European — UKB —
PSS008488 — — 440 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009386 — — 4,208 individuals — European UK (+ Ireland) UKB —
PSS008753 — — 2,200 individuals — European Italy (South Europe) UKB —
PSS010892 — — 4,334 individuals,
48.0 % Male samples
 Mean = 57.1 years
Sd = 8.0 years		 European white British UKB —
PSS010640 — — 1,952 individuals,
44.0 % Male samples
 Mean = 54.5 years
Sd = 8.6 years		 European Italian UKB —
PSS010388 — — 631 individuals,
31.0 % Male samples
 Mean = 53.8 years
Sd = 8.1 years		 East Asian Chinese UKB —
PSS007869 — — 1,407 individuals — African American or Afro-Caribbean Carribean UKB —